8tof.1 | SWISS-MODEL Template Library

Modelling
Repository
Tools
Documentation
Log in
Create Account

SMTL ID : 8tof.1

Rpd3S bound to an H3K36Cme3 modified nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-2-2-2-2-mer

Ligands

1 x UNK- UNK- ARG- UNK- UNK: Rco1(Non-covalent)

UNK-UNK-ARG-UNK-UNK.1:

8 residues within 4Å:

Chain K: Y.58, E.62, D.91, E.93
Chain L: E.103, L.104, H.107, E.111

5 PLIP interactions:

4 interactions with chain K, 1 interactions with chain L

Hydrogen bonds: K:Y.58
Salt bridges: K:E.62, K:D.91, K:E.93
Hydrophobic interactions: L:E.103

1 x UNK- UNK- UNK- LYS- UNK- UNK- UNK: histone N-terminal tail(Non-covalent)

UNK-UNK-UNK-LYS-UNK-UNK-UNK.2:

15 residues within 4Å:

Chain A: V.787, G.794, F.795
Chain B: G.37, P.39, D.109, H.151, G.159, F.160, H.188, F.215, R.280, L.281, Y.313
Ligands: ZN.3

10 PLIP interactions:

9 interactions with chain B, 1 interactions with chain A

Hydrophobic interactions: B:D.109, B:F.160, B:F.160, B:F.215, B:F.215, B:L.281, A:V.787
Hydrogen bonds: B:D.109, B:D.109, B:H.151

5 x ZN: ZINC ION(Non-covalent)

ZN.3:	6 residues within 4Å: Chain B: D.186, H.188, D.274, G.311, Y.313 Ligands: UNK-UNK-UNK-LYS-UNK-UNK-UNK.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.186, B:D.186, B:H.188, B:D.274
ZN.4:	4 residues within 4Å: Chain F: C.263, C.266, H.283, C.286 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.263, F:C.266, F:H.283, F:C.286
ZN.5:	4 residues within 4Å: Chain F: C.417, C.420, H.448, C.451 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.417, F:C.420, F:H.448, F:C.451
ZN.6:	4 residues within 4Å: Chain F: C.440, C.443, C.466, H.469 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.440, F:C.443, F:C.466, F:H.469
ZN.7:	5 residues within 4Å: Chain F: C.275, T.277, C.278, C.303, C.306 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.275, F:C.278, F:C.303

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Markert, J.W. et al., Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex. Nat Commun (2023)

Release Date

2024-01-17

Peptides

Transcriptional regulatory protein SIN3: A
Histone deacetylase RPD3: B
Chromatin modification-related protein EAF3: CD
Transcriptional regulatory protein RCO1: EF
Histone H3: IM
Histone H4: JN
Histone H2A: KO
Histone H2B 1.1: LP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

I
a

M
e

J
b

N
f

K
c

O
g

L
d

P
h

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

Transcriptional regulatory protein RCO1

Histone H3

Toggle Identical (IM)

Histone H4

Histone H2A

Histone H2B 1.1

Related Entries With Identical Sequence

1eqz.1 | 1f66.1 | 1hq3.1 | 1tzy.1 | 1u35.1 | 2aro.1 | 2cv5.1 | 2f8n.1 | 3lel.1 | 3lel.2 | 3nqu.1 | 3r45.1 | 4hga.1 | 4kgc.1 | 4ld9.1 | 4z2m.1 | 4zux.1 | 4zux.2 | 5c3i.1 | 5c3i.2 | 5c3i.3 | 5c3i.4 | 5c3i.5 | 5c3i.6 | 5e5a.1 | 5kgf.1 | 5o9g.1 | 5omx.1 | 5ong.1 | 5onw.1 more...less...

5oxv.1 | 5oy7.1 | 5x0x.1 | 5xf3.1 | 5xf4.1 | 5xf5.1 | 6buz.1 | 6e0c.1 | 6e0p.1 | 6ftx.1 | 6g0l.1 | 6hts.1 | 6i84.1 | 6j99.1 | 6kw3.1 | 6kw4.1 | 6kw5.1 | 6l9z.1 | 6la2.1 | 6la8.1 | 6la9.1 | 6lab.1 | 6ler.1 | 6ler.2 | 6ltj.1 | 6m3v.1 | 6m44.1 | 6m4d.1 | 6m4g.1 | 6m4h.1 | 6n1z.1 | 6n1z.2 | 6ne3.1 | 6nzo.1 | 6o1d.1 | 6o22.1 | 6o96.1 | 6om3.1 | 6om3.2 | 6pa7.1 | 6pwv.1 | 6pww.1 | 6pwx.1 | 6px1.1 | 6px3.1 | 6r0c.1 | 6r8y.1 | 6rny.1 | 6ryr.1 | 6ryu.1 | 6se0.1 | 6se6.1 | 6see.1 | 6sef.1 | 6seg.1 | 6t79.1 | 6t7a.1 | 6t7b.1 | 6t7c.1 | 6t7d.1 | 6tem.1 | 6upk.1 | 6upl.1 | 6v92.1 | 6vz4.1 | 6w5i.1 | 6w5m.1 | 6w5n.1 | 6wkr.1 | 6y5d.1 | 6zhx.1 | 6zhy.1 | 7dbp.1 | 7jo9.1 | 7joa.1 | 7k5x.1 | 7k5y.1 | 7k60.1 | 7k61.1 | 7k63.1 | 7kbd.1 | 7kbe.1 | 7kbf.1 | 7m1x.1 | 7mbm.1 | 7mbn.1 | 7nkx.1 | 7nky.1 | 7nl0.1 | 7otq.1 | 7pet.1 | 7peu.1 | 7pev.1 | 7pew.1 | 7pex.1 | 7pey.1 | 7pez.1 | 7pf0.1 | 7pf2.1 | 7pf3.1 | 7pf4.1 | 7pf5.1 | 7pf6.1 | 7pfa.1 | 7pfc.1 | 7pfd.1 | 7pfe.1 | 7pff.1 | 7pft.1 | 7pfu.1 | 7pfv.1 | 7pfw.1 | 7pfx.1 | 7pii.1 | 7r5r.1 | 7ssa.1 | 7tan.1 | 7u0g.1 | 7u0i.1 | 7u0j.1 | 7u46.1 | 7u47.1 | 7u4d.1 | 7ud5.1 | 7unc.1 | 7und.1 | 7unk.1 | 7ux9.1 | 7v90.1 | 7v96.1 | 7v9c.1 | 7v9j.1 | 7v9k.1 | 7v9s.1 | 7va4.1 | 7vcq.1 | 7vcq.2 | 7vcq.3 | 7vdt.1 | 7vdv.1 | 7vvu.1 | 7vvz.1 | 7x3t.1 | 7x3v.1 | 7x3w.1 | 7x3x.1 | 7xfc.1 | 7xfh.1 | 7xfi.1 | 7xfj.1 | 7xfl.1 | 7xfm.1 | 7xfn.1 | 7xnp.1 | 7y5u.1 | 7y5v.1 | 7y5w.1 | 7y60.1 | 7y61.1 | 7yi0.1 | 7yi1.1 | 7yi2.1 | 7yi3.1 | 7yi4.1 | 7yi5.1 | 7ywx.1 | 7yyh.1 | 7zi4.1 | 8a3y.1 | 8aag.1 | 8b0a.1 | 8bvw.1 | 8byq.1 | 8bz1.1 | 8dk5.1 | 8du4.1 | 8ett.1 | 8etv.1 | 8eu2.1 | 8eue.1 | 8euj.1 | 8evg.1 | 8evh.1 | 8evi.1 | 8evj.1 | 8g6g.1 | 8g6h.1 | 8g6q.1 | 8g6s.1 | 8ga8.1 | 8gpn.1 | 8h1t.1 | 8hpo.1 | 8hxx.1 | 8hxy.1 | 8hxz.1 | 8hy0.1 | 8ihn.1 | 8iht.1 | 8iqf.1 | 8iqg.1 | 8j6s.1 | 8j6t.1 | 8jh2.1 | 8jh3.1 | 8jh4.1 | 8jho.1 | 8kc7.1 | 8kd2.1 | 8kd3.1 | 8kd4.1 | 8kd5.1 | 8kd6.1 | 8kd7.1 | 8of4.1 | 8off.1 | 8pki.1 | 8pkj.1 | 8rbx.1 | 8sps.1 | 8spu.1 | 8svf.1 | 8syp.1 | 8t9f.1 | 8t9g.1 | 8t9h.1 | 8tas.1 | 8tb9.1 | 8thu.1 | 8u5h.1 | 8uw1.1 | 8v25.1 | 8v26.1 | 8v27.1 | 8v28.1 | 8vfx.1 | 8vfy.1 | 8vfz.1 | 8vg0.1 | 8vg1.1 | 8vg2.1 | 8vx5.1 | 8vx6.1 | 8w9c.1 | 8w9d.1 | 8w9e.1 | 8w9f.1 | 8x15.1 | 8x19.1 | 8x1c.1 | 8xjv.1 | 8xjv.2 | 8xjv.3 | 8xjv.4 | 8xjv.5 | 8xjv.6 | 8xjv.7 | 8xjv.8 | 8xjv.9 | 8xjv.11 | 8xjv.12 | 8xjv.24 | 8xjv.25 | 8xjv.26 | 8xjv.27 | 8xjv.28 | 8xjv.29 | 8xjv.30 | 8xjv.31 | 8xjv.32 | 8xjv.33 | 8xjv.34 | 8xjv.35 | 8xjv.36 | 8xjv.37 | 8xjv.38 | 8xjv.39 | 8xjv.40 | 8xjv.41 | 8xjv.42 | 8xjv.43 | 8xjv.44 | 8xjv.45 | 8xjv.46 | 8xjv.47 | 8xjv.48 | 8xjv.49 | 8xjv.50 | 8xjv.51 | 8xjv.52 | 8xjv.53 | 8xjv.54 | 8xjv.55 | 8xjv.56 | 8xjv.57 | 8xjv.58 | 8xjv.59 | 8xjv.60 | 8xjv.61 | 8xjv.62 | 8xjv.63 | 8xjv.64 | 8xjv.65 | 8xjv.66 | 8xjv.67 | 8xjv.68 | 8xjv.69 | 8xjv.70 | 8xjv.71 | 8xjv.72 | 8xjv.73 | 8xjv.74 | 8xjv.75 | 8xjv.76 | 8xjv.77 | 8xjv.78 | 8xjv.79 | 8xjv.80 | 8xjv.81 | 8xjv.82 | 8xjv.83 | 8xjv.93 | 8yjf.1 | 8yjm.1 | 8yti.1 | 8z50.1 | 9b3p.1 | 9fgq.1 | 9fh9.1 | 9gd0.1 | 9gd1.1 | 9gd2.1 | 9gd3.1

Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

Swiss Institute of BioinformaticsSIB
Schwede Group
Contact Us
Terms of use
Back to the Top